Debian Science Physics packages

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.

ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided.

This package contains the executables needed to perform calculations (however, pseudopotentials are not supplied). For a set of pseudopotentials, install the abinit-data package.

Axiom is useful for research and development of mathematical algorithms. It defines a strongly typed, mathematically correct type hierarchy. It has a programming language and a built-in compiler.

Axiom has been in development since 1973 and was sold as a commercial product. It has been released as free software.

Efforts are underway to extend this software to (a) develop a better user interface (b) make it useful as a teaching tool (c) develop an algebra server protocol (d) integrate additional mathematics (e) rebuild the algebra in a literate programming style (f) integrate logic programming (g) develop an Axiom Journal with refereed submissions.

This package contains the main program binary and all precompiled algebra and autoloadable modules.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This metapackage provides almost all of the programs and libraries contained in CERNLIB. Most people will likely want only a subset of these. A few extra CERNLIB programs, not of interest to many people, may be obtained via the cernlib-extras metapackage.

CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations.

CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian calculations as well. Features include:

Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:

• Density-Functional Theory (DFT) energies and forces
• Hartree-Fock (HF) energies and forces
• Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
• Random Phase Approximation (RPA) energies
• Gas phase or Periodic boundary conditions (PBC)
• Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave approach (GPW/GAPW)
• Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core corrected (NLCC) pseudopotentials, or all-electron calculations
• Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE
• Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS
• Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3
• Double-hybrid XC functionals including B2PLYP and B2GPPLYP
• Additional XC functionals via LibXC
• Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
• Non-local van der Waals corrections for XC functionals including B88-vdW, PBE-vdW and B97X-D
• DFT+U (Hubbard) correction
• Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and for MP2/RPA via Resolution-of-identity (RI)
• Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation
• Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer
• Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
• Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear scaling of molecular systems
• Excited states via time-dependent density-functional perturbation theory (TDDFPT)

Ab-initio Molecular Dynamics:

• Born-Oppenheimer Molecular Dynamics (BOMD)
• Ehrenfest Molecular Dynamics (EMD)
• PS extrapolation of initial wavefunction
• Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
• Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics (Second-Generation Car-Parrinello Molecular Dynamics (SGCP))

Mixed quantum-classical (QM/MM) simulations:

• Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part
• Linear-scaling electrostatic coupling treating of periodic boundary conditions
• Adaptive QM/MM

Further Features include:

• Single-point energies, geometry optimizations and frequency calculations
• Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations
• Global optimization of geometries
• Solvation via the Self-Consistent Continuum Solvation (SCCS) model
• Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations, density-functional tight-binding (DFTB) and self-consistent-polarization tight-binding (SCP-TB), with or without periodic boundary conditions
• Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats
• Metadynamics including well-tempered Metadynamics for Free Energy calculations
• Classical Force-Field (MM) simulations
• Monte-Carlo (MC) KS-DFT simulations
• Static (e.g. spectra) and dynamical (e.g. diffusion) properties
• ATOM code for pseudopotential generation
• Integrated molecular basis set optimization

CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).

DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

• an OpenGL window for immediate viewing
• the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
• the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
• a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

The European Theoretical Spectroscopy Facility (ETSF) is a European network dedicated to providing support and services for ongoing research in academic, government and industrial laboratories.

The ETSF is divided into 7 beamlines, each of which is concerned with a specific scientific topic:

• Optics ;
• Energy Loss Spectroscopy ;
• Quantum Transport ;
• Time-resolved Spectroscopy ;
• Photo-emission Spectroscopy ;
• Vibrational Spectroscopy ;
• X-Rays Spectroscopy.

To allow the adoption of its recommendations about standardization, the ETSF proposes different libraries and tools implementing or using these specifications, as well as widely usable pieces of software.

ETSF_IO is a library of F90 routines to read/write the ETSF file format. This package contains the user tools to:

• check file conformance to the specifications;
• extract data from files;
• merge multiple files from parallel runs, as specified in the specifications.

FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

Note that you will need the texlive-metapost package in order to use the MetaPost-based version of FeynMF.

Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.

It was developed for analyzing diffraction patterns, but can be also used in other fields, since concepts and operations specific for crystallography are separated from the rest of the program.

Fityk offers various nonlinear fitting methods, subtracting background, calibrating data, easy placement of peaks and changing peak parameters, automation of common tasks with scripts, and much more. The main advantage of the program is flexibility - parameters of peaks can be arbitrarily bound to each other, eg. the width of a peak can be an independent variable, can be the same as the width of another peak or can be given by a complicated - common to all peaks - formula.

libjs-sphinxdoc is necessary for the Javascript stuff in the documentation.

GEANT is a framework for simulating the passage of subatomic particles through matter, for instance, particle detectors. For maximum flexibility, GEANT simulations are performed by linking FORTRAN code supplied by the user with the GEANT library, then running the resulting executable.

This package includes gxint, a script that makes this linking step more convenient.

Gerris is a system for the solution of the partial differential equations describing fluid flow.

A brief summary of its main (current) features:

• Solves the time-dependent incompressible variable-density Euler, Stokes or Navier-Stokes equations
• Adaptive mesh refinement: the resolution is adapted dynamically to the features of the flow
• Entirely automatic mesh generation in complex geometries
• Second-order in space and time
• Unlimited number of advected/diffused passive tracers
• Flexible specification of additional source terms
• Portable parallel support using the MPI library
• Volume of Fluid advection scheme for interfacial flows

This package has MPI support built in.

The hkl library is a framework for diffraction computation and diffractometer control, heavily used at the SOLEIL synchrotron. It supports various types of diffractometer geometry: Eulerian 4-circle, Eulerian 6-circle, kappa 4-circle, kappa 6-circle, and z-axis geometry. For each of these it provides several numerically computed modes, such as bisector and constant psi.

This package provides a gui on top of the hkl library.

A density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods, atom-centered basis-functions or plane-waves.

Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data visualization and analysis. It is primarily intended for analysis of height field data obtained by microscopy techniques like

• Atomic Force Microscopy (AFM),
• Magnetic Force Microscopy (MFM),
• Scanning Tunneling Microscopy (STM),
• Near-field Scanning Optical Microscopy (SNOM or NSOM) and others. However, it can be used for arbitrary height field and image analysis.

This package contains the main application and its modules. It also contains a GNOME (and Xfce) thumbnailer which creates previews for all file types known to Gwyddion.

Maxima is a fully symbolic computation program. It is full featured doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter methods for finite group analysis, graphing, multiple precision floating point computation. It has a symbolic source level debugger for maxima code. Maxima is based on the original Macsyma developed at MIT in the 1970s. It is quite reliable, and has good garbage collection, and no memory leaks. It comes with hundreds of self tests.

This package contains the main executables and base system files.

This is an open source, portable, and extendible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

Meshlab can read files in these formats: PLY, STL, OFF, OBJ, 3DS, COLLADA and PTX. It can write PLY, STL, OFF, OBJ, 3DS, COLLADA, VRML, and DXF.

MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (HF)
• Density Functional Theory (DFT)
• Closed shell second-order Moeller-Plesset perturbation theory (MP2)

Additionally, it can compute energies for the following methods:

• Open shell MP2 and closed shell explicitly correlated MP2 theory (MP2-R12)
• Second order open shell pertubation theory (OPT2[2])
• Z-averaged pertubation theory (ZAPT2)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Package contains binaries.

OpenMX (Open source package for Material eXplorer) is a program package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials and pseudo-atomic localized basis functions. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as biomaterials, carbon nanotubes, magnetic materials, and nanoscale conductors.

OpticalRayTracer is an application that analyzes systems of lenses and mirrors. It uses optical principles and a virtual optical bench to predict the behavior of many kinds of ordinary and exotic lens types as well as flat and curved mirrors. OpticalRayTracer includes an advanced, easy-to-use interface that allows the user to rearrange the optical configuration by dragging objects around using the mouse.

OpticalRayTracer fully analyzes lens optical properties, including refraction and dispersion. The dispersion display uses color-coded light beams to simplify interpretation of the results.

OpticalRayTracer allows the creation of mirrors, flat and curved. In modern optical designs, mirrors often produce better results than lenses, for example in astronomical instruments. Such instruments can be roughed out in OpticalRayTracer's virtual workbench.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

PAW is an interactive program providing interactive graphical presentation and statistical and mathematical analysis tools. It is designed to work on objects familiar to physicists such as histograms, event files (Ntuples), vectors, etc.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes Paw++, an interactive program for use in analysis and graphical presentation. Paw++ is the same program as PAW (in the "paw" package), but with a more user-friendly Motif-based GUI, compiled against Lesstif in Debian.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (including analytical hessians for RHF)
• Closed shell Moeller-Plesset pertubation theory (MP2)
• Complete active space SCF (CASSCF)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

• Unrestricted open shell Hartree-Fock (UHF)
• Closed/open shell Moeller-Plesset pertubation theory (MP2)
• Closed shell explicitly correlated MP2 theory (MP2-R12) and spin-component scaled MP2 theory (SCS-MP2)
• Multireference configuration-interaction (MRCI)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T))
• Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
• Multireference coupled-cluster singles doubles (MRCCSD)
• Closed shell and general restricted open shell equation-of-motion coupled- cluster singles doubles (EOM-CCSD)

Further features include:

• Flexible, modular and customizable input format
• Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
• Internal coordinate geometry optimizer
• Harmonic frequencies calculations
• One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
• Utilization of molecular point-group symmetry to increase efficiency

PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.

This package provides the PyFR application.

PyMca is set of applications and Python libraries for analysis of X-ray fluorescence spectra.

The applications included in this package are:

• edfviewer - Display and inspection of data files in ESRF Data Format
• elementsinfo - Displays element specific X-ray data
• mca2edf - Converts files from SPEC MCA format to EDF
• peakidentifier - Displays X-ray fluorescence peaks in a given energy range
• pymcabatch - Batch fitting of spectra
• pymcapostbatch - Post-processing of batch fitting results
• pymca - Interactive data-analysis
• pymcaroitool - Region-of-interest (ROI) imaging tool

The PyMca toolkit can read data files in SPEC, ESRF data file (EDF), OMNIC, HDF5, AIFIRA and SupaVisio formats.

This are the scripts of the package.

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanism such as multiprocessing and SCOOP.

This package contains the modules for Python3.

SymPy is a Python library for symbolic mathematics (manipulation). It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries, except optionally for plotting support.

This package contains the Python 3 version of sympy.

Quantum ESPRESSO (formerly known as PWscf) is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

Features include:

• Ground-state single-point and band structure calculations using plane-wave self-consistent total energies, forces and stresses
• Separable norm-conserving and ultrasoft (Vanderbilt) pseudo-potentials, PAW (Projector Augmented Waves)
• Various exchange-correlation functionals, from LDA to generalized-gradient corrections (PW91, PBE, B88-P86, BLYP) to meta-GGA, exact exchange (HF) and hybrid functionals (PBE0, B3LYP, HSE)
• Car-Parrinello and Born-Oppenheimer Molecular Dynamics
• Structural Optimization including transition states and minimum energy paths
• Spin-orbit coupling and noncollinear magnetism
• Response properties including phonon frequencies and eigenvectors, effective charges and dielectric tensors, Infrared and Raman cross-sections, EPR and NMR chemical shifts
• Spectroscopic properties like K- and L1-edge X-ray Absorption Spectra (XAS) and electronic excitations

Debian-Electronics is now a separate Debian Pure Blend and allows a fine-grained control on the topics to install. To ease the transition, this package will install all user related tasks from Debian-Electronics.

This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains the 'siconos' tool allowing to compile and run Siconos programs/scripts in a single command.

Siconos is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems in C++ and in Python:

• Mechanical systems (rigid or solid) with unilateral contact and Coulomb friction and impact (nonsmooth mechanics, contact dynamics, multibody systems dynamics or granular materials).
• Switched Electrical Circuit such as electrical circuits with ideal and piecewise linear components: power converter, rectifier, Phase-Locked Loop (PLL) or Analog-to-Digital converter.
• Sliding mode control systems.
• Biology (Gene regulatory network). Other applications are found in Systems and Control (hybrid systems, differential inclusions, optimal control with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics.

This package contains tools to allow running, analysing, manipulating, exporting, and viewing the output of mechanical simulations.

Toulbar2 is an exact discrete optimization tool for Graphical Models such as Cost Function Networks, Markov Random Fields, Weighted Constraint Satisfaction Problems and Bayesian Nets.

V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows one to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

The Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints.

This package provides evolver variants built with different floating point formats (double, long double, quadruple) but with no X support.

The Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints.

This package provides evolver variants built with different floating point formats (double, long double, quadruple) and with an OpenGL/GLUT display.

OpenCTM — the Open Compressed Triangle Mesh file format — is a file format, a software library and a tool set for compression of 3D triangle meshes. The geometry is compressed to a fraction of comparable file formats, and the format is easily accessible through a simple, portable API.

This package contains the programs ctmconv and ctmview, used to convert and view OpenCTM files.

CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes example scripts for use by PAW or Paw++, and test scripts to make sure that the PAW or Paw++ programs behave correctly. You may run the examples and tests with the included paw-demos program.

This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics debtag and, depending on your focus, in the education-mathematics metapackage.

本元包是 Debian Pure Blend“Debian Science“（Debian 科学）的一部分，它将引入 与统计相关的软件包。作为一般的任务软件包，其目标是针对科学工作。具体来说， 该包依赖许多 R 软件包，以及其它对统计工作有意义的工具。除此之外，您还可以考 虑安装该包建议安装的 Debian 数学任务包以安装所有与数学相关的软件。

FDMNES calculates the spectra of different spectroscopies related to the real or virtual absorption of x-ray in material. It gives the absorption cross sections of photons around the ionization edge, that is in the energy range of XANES in the EXAFS. The calculation is performed with all conditions of rectilinear or circular polarization. In the same way, it calculates the structure factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD). FDMNES also allows the comparison of the simulated spectra to experimental ones with the help of objective criteria.

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

This is a metapackage depending on all libraries.

Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots etc) can be accomplished without any knowledge about VTK.

BLZPACK (for Block LancZos PACKage, release 04/00) is a standard Fortran 77 implementation of the block Lanczos algorithm intended for the solution of the standard eigenvalue problem Ax=µx or the generalized eigenvalue problem Ax=µBx, where A and B are real, sparse symmetric matrices, µ an eigenvalue and x an eigenvector.

The development of this eigensolver was motivated by the need to solve large, sparse, generalized problems from free vibration analyses in structural engineering. Several upgrades were performed afterwards aiming at the solution of eigenvalues problems from a wider range of applications.

Documentation: user's guide, technical report and comprehensive bibliography.

Install this package if you need to compile or link against BLZPACK.

The CLHEP package is a set of High Energy Physics specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra.

GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time.

ESPResSo is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems.

JFreeMesh is a 3D mesh library written in Java and providing a high level API for mesh manipulation. JFreeMesh is based on a descending mesh data structure but simulate a full connectivity mesh by providing optimized method to access to any upper mesh element by using the global mesh methods. Therefore,

 JFreeMesh allows to load a large amount of mesh elements for a small memory
foot print. JFreeMesh comes with a default mesh loader based on the GMSH file

format and provides, through the JFreeMesh-VTK package, an exporter to VTK.

JSPIS stands for Spacecraft Plasma Interaction System. SPIS project aims at developing a software toolkit for spacecraft-plasma interactions modelling.